Schiff base-dependent decarboxylations

In the case of decarboxylations, the negative charge produced in the decarboxylation step may be neutralized by some distal positive charge. This occurs in the case of Schiff base-dependent decarboxylations, thiamin pyrophosphate-dependent decarboxylations, and in a few other cases. Such systems are often referred to as electron sinks. ... 

The pH dependence of the kinetics of histidine decarboxylase (127) demonstrates that the histidine is zwitterionic when it binds to the enzyme. The extra proton on nitrogen must, of course, be removed before the Schiff base is formed. The carboxylate of Glu-197 at the active site may accept this proton. In turn, this same group may then be responsible for proton donation to the Schiff base following decarboxylation. This is consistent with the occurrence of retention of configuration in the overall replacement of-C02 by -H (128) and with studies of enzymes altered at Glu-197 (129). When Glu-197 is replaced by Asp, the protonation that follows decarboxylation occasionally occurs on the pyruvate side, thus giving rise to decarboxylation-dependent transamination (129). 

Lactobacillus delbrueckii. In 1953, Rodwell suggested that the histidine decarboxylase of Lactobacillus 30a was not dependent upon pyridoxal phosphate (11). Rodwell based his suggestion upon the fact that the organism lost its ability to decarboxylate ornithine but retained high histidine decarboxylase activity when grown in media deficient in pyridoxine. It was not until 1965 that E. E. Snell and coworkers (12) isolated the enzyme and showed that it was, indeed, free of pyridoxal phosphate. Further advances in characterization of the enzyme were made by Riley and Snell (13) and Recsei and Snell (14) who demonstrated the existence of a pyruvoyl residue and the participation of the pyruvoyl residue in histidine catalysis by forming a Schiff base intermediate in a manner similar to pyridoxal phosphate dependent enzymes. Recent studies by Hackert et al. (15) established the subunit structure of the enzyme which is similar to the subunit structure of a pyruvoyl decarboxylase of a Micrococcus species (16). 

Decarboxylation of p-oxoacids. Beta-oxoacids such as oxaloacetic acid and acetoacetic acid are unstable, their decarboxylation being catalyzed by amines, metal ions, and other substances. Catalysis by amines depends upon Schiff base formation,232 while metal ions form chelates in which the metal assists in electron withdrawal to form an enolate anion.233 235... 

Below the structures of the adducts in Eq. 14-20 are those of a 2-oxo acid and a (3-ketol with arrows indicating the electron flow in decarboxylation and in the aldol cleavage. The similarities to the thiamin-dependent cleavage reaction are especially striking if one remembers that in some aldolases and decarboxylases the substrate carbonyl group is first converted to an N-proto-nated Schiff base before the bond cleavage. 

In PLP-dependent enzymatic reactions, the Schiff base formed by reaction of the substrate with PLP provides an electron sink for stabilization of the negative charge that results from the bond-breaking process required in the reaction (racemization, decarboxylation, aldol reaction, elimination, etc.). The elegant work of Walsh and coworkers provided evidence that, subsequent to Schiff base formation, a common intermediate is formed from several different alanine analogues that are alanine racemase inhibitors. From this they proposed the elimination-Michael addition sequence shown in Figure 14 as the mechanism for inhibition166. 

ALA synthase is a pyridoxal phosphate-dependent enzyme and promotes Schiff-base formation between its coenzyme and glycine (67 in Fig. 37). Nucleophilicity at C-2 of the glycine could be generated either by decarboxylation or by abstraction of a proton. In the first case 5-aminolaevulinic acid would retain both methylene protons of glycine, in the second, one of the protons would be lost to the medium (Fig. 37). Acylation of the pyridoxal-bound intermediate (68 or 69) by succinyl-CoA would constitute the next step and this could be followed either by direct hydrolysis of the Schiff-base or by decarboxylation with subsequent hydrolysis depending on which course was chosen in the first stage of the reaction. 

According to O Leary the kl2/k13 KIE (for loss of C02) varies between 1.01 and 1.03 for a variety of pyridoxal phosphate-dependent decarboxylases141. Assuming (based on models) that the intrinsic KIE is ca 1.05 for the decarboxylation step k5, these numbers suggest that decarboxylation is not totally rate-determining, rather Schiff-base interchange (transimination) and C—C scission are both participating in rate-limitation ( 4 k5) see Scheme 13. 

The ring nitrogen of pyridoxal phosphate exerts a strong electron withdrawing effect on the aldimine, and this leads to weakening of all three bonds about the a-carbon of the substrate. In nonenzymic reactions, all the possible pyridoxal-catalyzed reactions are observed - a-decarboxylation, aminotrans-fer, racemization and side-chain elimination, and replacement reactions. By contrast, enzymes show specificity for the reaction pathway followed which bond is cleaved will depend on the orientation of the Schiff base relative to reactive groups of the catalytic site. As discussed in Section 9.3.1.5, reaction specificity is not complete, and a number of decarboxylases also undergo transamination. 

Can we apply any of this information from non-enzymatic catalysis to decarboxylating enzymes Some decarboxylases do form Schiff bases with their substrates, and some are dependent on metal ions. The acetone-forming fermentation of Clostridium acetobutylicum requires large amounts of acetoacetate decarboxylase (Eq. 13-44). 

The basic decarboxylation mechanism is analogous to mechanisms of other PLP-dependent processes (Scheme VIII) 101-104). PLP is initially bound covalently to the enzyme via a Schiff base linkage to a lysine amino group. Other functional groups of PLP, particularly the phosphate, form strong noncovalent interactions with the enzyme. The substrate binds and reacts to form a bound PLP-substrate Schiff base. 

The catalytic strategy is familiar from our discussion of PLP-dependent reactions reaction via a Schiff base, probable medium control of the decarboxylation, and desolvation of the carboxyl group on binding to the enzyme. What is most surprising is that pyruvate, with its very small electron sink, works as efficiently as PLP, which allows for more extensive electron delocalization. The specialness of PLP in enzymic catalysis must lie in other factors. 

All known reactions of PLP-containing enzymes can be described mechanistically in the same way-formation of a planar Schiff base or aldimine intermediate, followed by formation of a resonance-stabilized carbanion with a quinoid structure, as shown in Figure 20,15. Depending on the bond labilized, formation of the aldimine can lead to a transamination (as shown in Figure 20.15), to decarboxylation, to racemization, or to numerous side chain modifications. 

The enzymes, amino acid decarboxylases are pyridoxal phosphate- dependent enzymes. Pyridoxal phosphate forms a Schiff s base with e amino acid so as to stabilise the a-carbanion formed by the cleavage of bond between carboxyl and a-carbon atom. The physiologically active amines epinephrine, nor-epinephrine, dopamine, serotonin, y-amino butyrate and histamine are formed through decarboxylation of the corresponding precursor amino acids... 

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